Background: malaria is a serious problem in the Amazonas state, especially in areas near forests. Indigenous populations living in these areas are very vulnerable to malaria infection. In addition, the disease severely affects children because their immune system is less well developed, and thus causes more severe symptoms. Therefore, the intersection between these two groups, indigenous people and children, is characterized by an important public health problem. The objective is to identify the factors associated with malaria in indigenous children in the Amazonas state, Brazil, from 2007 to 2018.Methods: This is an epidemiological, quantitative and cross-sectional study involving children under 15 years, and using data from health system notifications between 2007 and 2018, with the Amazonas state, Brazil, as a place of residence and probable infection setting. The variables are clinical-epidemiological, laboratorial and case follow-up, which were analyzed then stratified as to whether the case involved indigenous children or those of other races and entries for which no race data was given. The estimation of Odds Ratio with a confidence interval was obtained by multivariate logistic regression. Results: the factors associated with malaria in indigenous children were attributed to being of the female sex, age from 0 to 4 years, passive case surveillance, high load of parasitemia or lack of data regarding the level of parasitemia, parasitic forms containing Plasmodium falciparum were more frequent, as well as timeliness of treatment, which corresponds to the time between the onset of symptoms and the start of treatment being less than 48 hours. Conclusion: the factors associated with malaria in indigenous children highlight the difference in race, suggest more severity of the disease and more malarial infections in this population, and, as a result, malaria has a great impact on the health of the indigenous children.